Table 9.

A Selection of Available Tools for Phylogenetic Tests of Positive Selection.

Tool	Description	Online tutorials	Models implemented to test for positive selection	Language required?	OpenMP/MPI?	Same models as in CODEML?	Citations
CODEML	Software that can be used to detect positively selected protein-coding genes and infer parameters of codon-substitution models by fitting SM, BM, and BSM using ML	GitHub: https://github.com/abacus-gene/paml-tutorial	SM: M0, M1a, M2a, M7, M8, M8a BM: M0, two-ratio model, free-ratio model BSM: A, A-null	Bash scripting	No	–	Yang (2007)
EasyCodeML	Visual software that implements some CODEML models for detecting selection in molecular evolutionary analysis	GitHub: https://github.com/BioEasy/EasyCodeML	SM: M0, M1a, M2a, M7, M8 BM: M0, two-ratio model, free-ratio model BSM: A, A-null	No, it is a Java-based GUI	NA	Yes	Gao et al. (2019)
ete-evol	Software that automates the use of preconfigured evolutionary models that are part of CODEML and SLR	http://etetoolkit.org/documentation/ete-evol/	SM: M0, M1a, M2a, M7, M8 BM: M0, two-ratio model, free-ratio model BSM: A, A-null	Bash scripting	Yes	Yes	Huerta-Cepas et al. (2016)
FastCodeML	Software that optimizes positive selection inference by parallelizing the BSM in CODEML	No	BSM: A	Bash scripting	Yes	Yes, but optimized to be parallelized	Valle et al. (2014)
HyPhy/Datamonkey	Software for comparative sequence analysis with stochastic evolutionary models	http://hyphy.org/	SM: SLAC, FEL, MEME BSM: aBSREL	HyPhy Batch Language (HBL) + Bash scripting	Yes	No	Kosakovsky Pond et al. (2005)
SLR	Software that detects sites in the alignment that are unusually conserved and/or unusually variable	No	SM: SLR	Bash scripting	No	No	Massingham and Goldman (2005)

Note.—BM, branch models; BSM, branch-site model; SM, site models.